SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching P05661 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MPKPVANQEDEDPTPYLFVSLEQRRIDQSKPYDSKKSCWIPDEKEGYLLG    50
  51  EIKATKGDIVSVGLQGGEVRDIKSEKVEKVNPPKFEKIEDMADMTVLNTP   100
 101  CVLHNLRQRYYAKLIYTYSGLFCVAINPYKRYPVYTNRCAKMYRGKRRNE   150
 151  VPPHIFAISDGAYVDMLTNHVNQSMLITGESGAGKTENTKKVIAYFATVG   200
 201  ASKKTDEAAKSKGSLEDQVVQTNPVLEAFGNAKTVRNDNSSRFGKFIRIH   250
 251  FGPTGKLAGADIETYLLEKARVISQQSLERSYHIFYQIMSGSVPGVKDIC   300
 301  LLTDNIYDYHIVSQGKVTVASIDDAEEFSLTDQAFDILGFTKQEKEDVYR   350
 351  ITAAVMHMGGMKFKQRGREEQAEQDGEEEGGRVSKLFGCDTAELYKNLLK   400
 401  PRIKVGNEFVTQGRNVQQVTNSIGALCKGVFDRLFKWLVKKCNETLDTQQ   450
 451  KRQHFIGVLDIAGFEIFEYNGFEQLCINFTNEKLQQFFNHIMFVMEQEEY   500
 501  KKEGINWDFIDFGMDLLACIDLIEKPMGILSILEEESMFPKATDQTFSEK   550
 551  LTNTHLGKSAPFQKPKPPKPGQQAAHFAIAHYAGCVSYNITGWLEKNKDP   600
 601  LNDTVVDQFKKSQNKLLIEIFADHAGQSGGGEQAKGGRGKKGGGFATVSS   650
 651  AYKEQLNSLMTTLRSTQPHFVRCIIPNEMKQPGVVDAHLVMHQLTCNGVL   700
 701  EGIRICRKGFPNRMMYPDFKMRYQILNPRGIKDLDCPKKASKVLIESTEL   750
 751  NEDLYRLGHTKVFFRAGVLGQMEEFRDERLGKIMSWMQAWARGYLSRKGF   800
 801  KKLQEQRVALKVVQRNLRKYLQLRTWPWYKLWQKVKPLLNVSRIEDEIAR   850
 851  LEEKAKKAEELHAAEVKVRKELEALNAKLLAEKTALLDSLSGEKGALQDY   900
 901  QERNAKLTAQKNDLENQLRDIQERLTQEEDARNQLFQQKKKADQEISGLK   950
 951  KDIEDLELNVQKAEQDKATKDHQIRNLNDEIAHQDELINKLNKEKKMQGE  1000
1001  TNQKTGEELQAAEDKINHLNKVKAKLEQTLDELEDSLEREKKVRGDVEKS  1050
1051  KRKVEGDLKLTQEAVADLERNKKELEQTIQRKDKELSSITAKLEDEQVVV  1100
1101  LKHQRQIKELQARIEELEEEVEAERQARAKAEKQRADLARELEELGERLE  1150
1151  EAGGATSAQIELNKKREAELSKLRRDLEEANIQHESTLANLRKKHNDAVA  1200
1201  EMAEQVDQLNKLKAKAEHDRQTCHNELNQTRTACDQLGRDKAAQEKIAKQ  1250
1251  LQHTLNEVQSKLDETNRTLNDFDASKKKLSIENSDLLRQLEEAESQVSQL  1300
1301  SKIKISLTTQLEDTKRLADEESRERATLLGKFRNLEHDLDNLREQVEEEA  1350
1351  EGKADLQRQLSKANAEAQVWRSKYESDGVARSEELEEAKRKLQARLAEAE  1400
1401  ETIESLNQKCIGLEKTKQRLSTEVEDLQLEVDRANAIANAAEKKQKAFDK  1450
1451  IIGEWKLKVDDLAAELDASQKECRNYSTELFRLKGAYEEGQEQLEAVRRE  1500
1501  NKNLADEVKDLLDQIGEGGRNIHEIEKARKRLEAEKDELQAALEEAEAAL  1550
1551  EQEENKVLRAQLELSQVRQEIDRRIQEKEEEFENTRKNHQRALDSMQASL  1600
1601  EAEAKGKAEALRMKKKLEADINELEIALDHANKANAEAQKNIKRYQQQLK  1650
1651  DIQTALEEEQRARDDAREQLGISERRANALQNELEESRTLLEQADRGRRQ  1700
1701  AEQELADAHEQLNEVSAQNASISAAKRKLESELQTLHSDLDELLNEAKNS  1750
1751  EEKAKKAMVDAARLADELRAEQDHAQTQEKLRKALEQQIKELQVRLDEAE  1800
1801  ANALKGGKKAIQKLEQRVRELENELDGEQRRHADAQKNLRKSERRVKELS  1850
1851  FQSEEDRKNHERMQDLVDKLQQKIKTYKRQIEEAEEIAALNLAKFRKAQQ  1900
1901  ELEEAEERADLAEQAISKFRAKGRAGSVGRGASPAPRATSVRPQFDGLAF  1950
1951  PPRFDLAPENEF                                        1962

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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